WHAT IF Check report

This file was created 2012-01-25 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2kbu.ent

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

  13 ARG   (  13-)  A  1   N   bound to   12 CFD   (  12-)  A  1   C
  43 ARG   (  13-)  A  2   N   bound to   42 CFD   (  12-)  A  2   C
  73 ARG   (  13-)  A  3   N   bound to   72 CFD   (  12-)  A  3   C
 104 ARG   (  13-)  A  4   N   bound to  103 CFD   (  12-)  A  4   C
 135 ARG   (  13-)  A  5   N   bound to  134 CFD   (  12-)  A  5   C
 166 ARG   (  13-)  A  6   N   bound to  165 CFD   (  12-)  A  6   C
 197 ARG   (  13-)  A  7   N   bound to  196 CFD   (  12-)  A  7   C
 228 ARG   (  13-)  A  8   N   bound to  227 CFD   (  12-)  A  8   C
 259 ARG   (  13-)  A  9   N   bound to  258 CFD   (  12-)  A  9   C
 290 ARG   (  13-)  A 10   N   bound to  289 CFD   (  12-)  A 10   C
 321 ARG   (  13-)  A 11   N   bound to  320 CFD   (  12-)  A 11   C
 352 ARG   (  13-)  A 12   N   bound to  351 CFD   (  12-)  A 12   C
 383 ARG   (  13-)  A 13   N   bound to  382 CFD   (  12-)  A 13   C
 414 ARG   (  13-)  A 14   N   bound to  413 CFD   (  12-)  A 14   C
 445 ARG   (  13-)  A 15   N   bound to  444 CFD   (  12-)  A 15   C

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

  12 CFD   (  12-)  A
  42 CFD   (  12-)  A
  72 CFD   (  12-)  A
 103 CFD   (  12-)  A
 134 CFD   (  12-)  A
 165 CFD   (  12-)  A
 196 CFD   (  12-)  A
 227 CFD   (  12-)  A
 258 CFD   (  12-)  A
 289 CFD   (  12-)  A 1
 320 CFD   (  12-)  A 1
 351 CFD   (  12-)  A 1
 382 CFD   (  12-)  A 1
 413 CFD   (  12-)  A 1
 444 CFD   (  12-)  A 1

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 LYS   (   1-)  A    Zero
   2 LEU   (   2-)  A    Zero
   3 PRO   (   3-)  A    Zero
   4 PRO   (   4-)  A    Zero
   5 GLY   (   5-)  A    Zero
   6 TRP   (   6-)  A    Zero
   7 GLU   (   7-)  A    Zero
   8 LYS   (   8-)  A    Zero
   9 ARG   (   9-)  A    Zero
  10 MET   (  10-)  A    Zero
  11 SER   (  11-)  A    Zero
  12 CFD   (  12-)  A    Zero
  13 ARG   (  13-)  A    Zero
  14 VAL   (  14-)  A    Zero
  15 TYR   (  15-)  A    Zero
  16 TYR   (  16-)  A    Zero
  17 PHE   (  17-)  A    Zero
  18 ASN   (  18-)  A    Zero
  19 HIS   (  19-)  A    Zero
  20 ILE   (  20-)  A    Zero
  21 THR   (  21-)  A    Zero
  22 ASN   (  22-)  A    Zero
  23 ALA   (  23-)  A    Zero
  24 SER   (  24-)  A    Zero
  25 GLN   (  25-)  A    Zero
And so on for a total of 463 lines.

Geometric checks

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.644
Model 2 : 0.649
Model 3 : 0.651
Model 4 : 0.639
Model 5 : 0.642
Model 6 : 0.663
Model 7 : 0.652
Model 8 : 0.661
Model 9 : 0.655
Model 10 : 0.649
Model 11 : 0.638
Model 12 : 0.628
Model 13 : 0.662
Model 14 : 0.639
Model 15 : 0.638

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

  22 ASN   (  22-)  A     -C    N    CA  129.19    4.2
  31 GLY   (  31-)  A     -C    N    CA  128.58    4.7
  43 ARG   (  13-)  A      CD   NE   CZ  129.26    4.2
  58 ARG   (  28-)  A      CD   NE   CZ  129.05    4.1
  59 PRO   (  29-)  A      N    CA   C   123.43    4.7
  59 PRO   (  29-)  A      CD   N    CA  100.51   -8.2
  67 GLU   (   7-)  A     -C    N    CA  130.33    4.8
 100 ARG   (   9-)  A      CB   CG   CD  105.57   -4.3
 113 ASN   (  22-)  A     -C    N    CA  129.85    4.5
 129 GLU   (   7-)  A     -C    N    CA  129.96    4.6
 144 ASN   (  22-)  A      C    CA   CB  118.24    4.3
 166 ARG   (  13-)  A      CD   NE   CZ  129.23    4.2
 181 ARG   (  28-)  A      CD   NE   CZ  129.21    4.2
 206 ASN   (  22-)  A      C    CA   CB  118.42    4.4
 215 GLY   (  31-)  A     -C    N    CA  127.88    4.3
 228 ARG   (  13-)  A      CD   NE   CZ  129.71    4.5
 253 GLU   (   7-)  A     -C    N    CA  130.74    5.0
 264 ASN   (  18-)  A      ND2  CG   OD1 118.46   -4.1
 274 ARG   (  28-)  A      C    CA   CB  117.77    4.0
 290 ARG   (  13-)  A 1    CD   NE   CZ  128.95    4.0
 305 ARG   (  28-)  A 1   -C    N    CA  131.10    5.2
 305 ARG   (  28-)  A 1    C    CA   CB  119.70    5.1
 305 ARG   (  28-)  A 1    CD   NE   CZ  129.27    4.2
 306 PRO   (  29-)  A 1    CD   N    CA  103.37   -6.2
 308 GLY   (  31-)  A 1   -C    N    CA  130.07    5.6
 352 ARG   (  13-)  A 1    CD   NE   CZ  129.07    4.1
 356 PHE   (  17-)  A 1    CA   CB   CG  119.38    5.6
 361 ASN   (  22-)  A 1   -C    N    CA  129.34    4.2
 377 GLU   (   7-)  A 1   -C    N    CA  129.97    4.6
 398 ARG   (  28-)  A 1    CD   NE   CZ  130.83    5.1
 418 PHE   (  17-)  A 1    CA   CB   CG  118.47    4.7
 463 GLY   (  31-)  A 1   -C    N    CA  127.95    4.3

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 1.222
Model 2 : 1.326
Model 3 : 1.247
Model 4 : 1.268
Model 5 : 1.258
Model 6 : 1.267
Model 7 : 1.212
Model 8 : 1.244
Model 9 : 1.339
Model 10 : 1.430
Model 11 : 1.233
Model 12 : 1.221
Model 13 : 1.301
Model 14 : 1.210
Model 15 : 1.207

Note: Per-model averages for chirality check

The table below gives the per-model improper dihedral RMS Z-scores.

Model 1 : 1.235
Model 2 : 1.335
Model 3 : 1.055
Model 4 : 1.305
Model 5 : 1.160
Model 6 : 1.175
Model 7 : 1.058
Model 8 : 1.322
Model 9 : 1.060
Model 10 : 1.279
Model 11 : 1.013
Model 12 : 1.070
Model 13 : 1.122
Model 14 : 1.056
Model 15 : 0.974

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

  59 PRO   (  29-)  A    4.14

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  67 GLU   (   7-)  A    4.72
 242 GLU   (  27-)  A    4.69
 377 GLU   (   7-)  A 1   4.62
  97 TRP   (   6-)  A    4.59
 345 TRP   (   6-)  A 1   4.13
   7 GLU   (   7-)  A    4.06
 304 GLU   (  27-)  A 1   4.05
 221 TRP   (   6-)  A    4.02

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 358 HIS   (  19-)  A 1    CB   6.19
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.225

Torsion-related checks

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -1.211
Model 2 : -1.884
Model 3 : -3.598
Model 4 : -4.016
Model 5 : -1.265
Model 6 : -0.708
Model 7 : -3.125
Model 8 : -3.263
Model 9 : -2.400
Model 10 : -3.264
Model 11 : -2.375
Model 12 : -3.712
Model 13 : -2.903
Model 14 : -0.452
Model 15 : 0.721

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

  59 PRO   (  29-)  A    -3.1
 274 ARG   (  28-)  A    -2.6
   4 PRO   (   4-)  A    -2.4
 284 GLU   (   7-)  A 1   -2.3
 147 GLN   (  25-)  A    -2.3
 254 LYS   (   8-)  A    -2.3
 305 ARG   (  28-)  A 1   -2.3
 285 LYS   (   8-)  A 1   -2.2
 377 GLU   (   7-)  A 1   -2.2
 378 LYS   (   8-)  A 1   -2.2
 243 ARG   (  28-)  A    -2.1
 364 GLN   (  25-)  A 1   -2.1
 408 GLU   (   7-)  A 1   -2.1
 133 SER   (  11-)  A    -2.1
  99 LYS   (   8-)  A    -2.1
 409 LYS   (   8-)  A 1   -2.1
  67 GLU   (   7-)  A    -2.1
  98 GLU   (   7-)  A    -2.1
 102 SER   (  11-)  A    -2.1
 315 GLU   (   7-)  A 1   -2.0
 416 TYR   (  15-)  A 1   -2.0
 316 LYS   (   8-)  A 1   -2.0
 230 TYR   (  15-)  A    -2.0
 253 GLU   (   7-)  A    -2.0
 392 ASN   (  22-)  A 1   -2.0
 267 THR   (  21-)  A    -2.0
 361 ASN   (  22-)  A 1   -2.0
 192 LYS   (   8-)  A    -2.0
  58 ARG   (  28-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

   4 PRO   (   4-)  A  Poor phi/psi
  22 ASN   (  22-)  A  Poor phi/psi
  52 ASN   (  22-)  A  Poor phi/psi
  59 PRO   (  29-)  A  Poor phi/psi
  82 ASN   (  22-)  A  Poor phi/psi
  90 SER   (  30-)  A  Poor phi/psi
 113 ASN   (  22-)  A  Poor phi/psi
 121 SER   (  30-)  A  Poor phi/psi
 151 PRO   (  29-)  A  Poor phi/psi
 152 SER   (  30-)  A  Poor phi/psi
 175 ASN   (  22-)  A  Poor phi/psi
 182 PRO   (  29-)  A  Poor phi/psi
 206 ASN   (  22-)  A  Poor phi/psi
 214 SER   (  30-)  A  Poor phi/psi
 237 ASN   (  22-)  A  Poor phi/psi
 244 PRO   (  29-)  A  Poor phi/psi
 245 SER   (  30-)  A  Poor phi/psi
 274 ARG   (  28-)  A  Poor phi/psi
 276 SER   (  30-)  A  Poor phi/psi
 299 ASN   (  22-)  A 1 Poor phi/psi
 305 ARG   (  28-)  A 1 Poor phi/psi
 306 PRO   (  29-)  A 1 Poor phi/psi
 330 ASN   (  22-)  A 1 Poor phi/psi
 361 ASN   (  22-)  A 1 Poor phi/psi
 369 SER   (  30-)  A 1 Poor phi/psi
 392 ASN   (  22-)  A 1 Poor phi/psi
 423 ASN   (  22-)  A 1 Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.526

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.526

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -3.762
Model 2 : -5.621
Model 3 : -3.088
Model 4 : -2.056
Model 5 : -1.690
Model 6 : -6.925
Model 7 : -2.823
Model 8 : -4.168
Model 9 : -4.593
Model 10 : -6.081
Model 11 : -5.971
Model 12 : -4.710
Model 13 : -5.275
Model 14 : -6.291
Model 15 : -4.827

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   4 PRO   (   4-)  A      0
  10 MET   (  10-)  A      0
  11 SER   (  11-)  A      0
  12 CFD   (  12-)  A      0
  13 ARG   (  13-)  A      0
  14 VAL   (  14-)  A      0
  19 HIS   (  19-)  A      0
  23 ALA   (  23-)  A      0
  26 PHE   (  26-)  A      0
  30 SER   (  30-)  A      0
  31 GLY   (  31-)  A      0
  32 LYS   (   1-)  A      0
  33 PRO   (   3-)  A      0
  34 PRO   (   4-)  A      0
  36 TRP   (   6-)  A      0
  40 MET   (  10-)  A      0
  41 SER   (  11-)  A      0
  42 CFD   (  12-)  A      0
  43 ARG   (  13-)  A      0
  44 VAL   (  14-)  A      0
  49 HIS   (  19-)  A      0
  52 ASN   (  22-)  A      0
  53 ALA   (  23-)  A      0
  54 SER   (  24-)  A      0
  55 GLN   (  25-)  A      0
And so on for a total of 314 lines.

Warning: Backbone conformation Z-score low

A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is unusual.

Backbone conformation Z-score : -2.040

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.042

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 6.889
Model 2 : 7.698
Model 3 : 6.555
Model 4 : 6.607
Model 5 : 6.583
Model 6 : 6.956
Model 7 : 7.365
Model 8 : 7.253
Model 9 : 7.531
Model 10 : 7.164
Model 11 : 7.341
Model 12 : 7.068
Model 13 : 7.221
Model 14 : 6.816
Model 15 : 6.456

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  59 PRO   (  29-)  A    0.50 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  59 PRO   (  29-)  A   172.1 envelop N (180 degrees)
 213 PRO   (  29-)  A  -133.2 half-chair C-delta/C-gamma (-126 degrees)
 306 PRO   (  29-)  A 1 -172.8 envelop N (180 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

 154 LYS   (   1-)  A      NZ  <->  184 GLY   (  31-)  A      C      0.11    2.99
  98 GLU   (   7-)  A      CD  <->   99 LYS   (   8-)  A      NZ     0.10    3.00
 346 GLU   (   7-)  A 1    OE2 <->  358 HIS   (  19-)  A 1    NE2    0.10    2.60
 185 LYS   (   1-)  A      NZ  <->  211 GLU   (  27-)  A      OE2    0.09    2.61
  62 LYS   (   1-)  A      NZ  <->   87 GLU   (  27-)  A      OE2    0.09    2.61
 100 ARG   (   9-)  A      NH2 <->  108 PHE   (  17-)  A      CD1    0.09    3.01
 371 LYS   (   1-)  A 1    NZ  <->  397 GLU   (  27-)  A 1    CD     0.08    3.02
 123 LYS   (   1-)  A      NZ  <->  149 GLU   (  27-)  A      OE1    0.08    2.62
 377 GLU   (   7-)  A 1    OE2 <->  379 ARG   (   9-)  A 1    NH1    0.08    2.62
 123 LYS   (   1-)  A      NZ  <->  149 GLU   (  27-)  A      CD     0.08    3.02
 433 LYS   (   1-)  A 1    N   <->  478 GLY   (  31-)  A 1    O''    0.07    2.63
  13 ARG   (  13-)  A      NH2 <->   27 GLU   (  27-)  A      OE2    0.07    2.63
 439 GLU   (   7-)  A 1    OE2 <->  451 HIS   (  19-)  A 1    ND1    0.07    2.63
 315 GLU   (   7-)  A 1    CD  <->  316 LYS   (   8-)  A 1    NZ     0.07    3.03
   7 GLU   (   7-)  A      OE2 <->   19 HIS   (  19-)  A      ND1    0.07    2.63
 129 GLU   (   7-)  A      OE2 <->  141 HIS   (  19-)  A      ND1    0.07    2.63
  98 GLU   (   7-)  A      OE1 <->   99 LYS   (   8-)  A      NZ     0.07    2.63
 160 GLU   (   7-)  A      OE2 <->  172 HIS   (  19-)  A      ND1    0.07    2.63
  98 GLU   (   7-)  A      OE2 <->   99 LYS   (   8-)  A      NZ     0.07    2.63
 321 ARG   (  13-)  A 1    NH2 <->  335 GLU   (  27-)  A 1    OE2    0.07    2.63
 130 LYS   (   8-)  A      NZ  <->  153 GLY   (  31-)  A      O      0.07    2.63
 247 LYS   (   1-)  A      NZ  <->  273 GLU   (  27-)  A      OE2    0.07    2.63
 222 GLU   (   7-)  A      OE2 <->  234 HIS   (  19-)  A      ND1    0.07    2.63
 191 GLU   (   7-)  A      OE2 <->  203 HIS   (  19-)  A      ND1    0.07    2.63
 397 GLU   (  27-)  A 1    OE2 <->  398 ARG   (  28-)  A 1    NH2    0.06    2.64
And so on for a total of 109 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.215

Note: Per-model averages for inside/outside residue distributi ...heck















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Warning: Structural average packing environment a bit worrysome

Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Per-model averages for NQA















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure